VILL

protein-coding

villin like, the group of Gelsolin/villins

Gene summary

The protein encoded by this gene belongs to the villin/gelsolin family. It contains 6 gelsolin-like repeats and a headpiece domain. It may play a role in actin-bundling. [provided by RefSeq, Jul 2008]

MANE transcript

NM_015873.4

Inheritance

—

ClinVar variants

U:135B:15

Top phenotype

VILL-related disorder

gnomAD constraint

pLI —, LoF o/e 0.84

Max pathogenic AF

—

Genomic locus

chr3:37,988,059-38,007,188

External References & Databases

Ensembl (ENSG00000136059)

Transcript & Mutation Effects

hg38 • Region Span ~19.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to VILL variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 135

not providedTotal: 2

VILL-related disorderTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015873.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	1 clinvar		3
missense			127 clinvar	11 clinvar	1 clinvar	139
nonsense			1 clinvar			1
start loss						0
frameshift				2 clinvar		2
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	135	14	1	150

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 58 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015873.4	RefSeq	NP_056957.3	19	MANE Select
ENST00000383759.7	Ensembl	ENSP00000373266.2	19	MANE Select
NM_001370264.1	RefSeq	NP_001357193.1	15	Standard
NM_001370265.1	RefSeq	NP_001357194.1	14	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cytoskeleton organization
actin filament capping

Molecular Function

structural constituent of cytoskeleton
actin filament binding

Cellular Component

actin cytoskeleton

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000283713
Coding exons: 19
Length: 19130
Individuals with no LoFs: 125170
Homozygous LoFs: 4
Heterozygous LoFs: 574
Defined: 125748
p: 0.00230

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.345	485	507	0.957	0.0000285	5610
Missense (PolyPhen)		143	153.78	0.92991		1838
Synonymous	0.666	192	204	0.941	0.0000117	1658
Loss of Function	1.04	39	46.7	0.836	0.00000234	496

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0086	0.0085	notable
Latino/Admixed American	0.0019	0.0018	notable
Ashkenazi Jewish	0.00050	0.00050	rare
East Asian	0.0042	0.0041	notable
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.0011	0.0011	notable
South Asian	0.0051	0.0050	notable
Other	0.0026	0.0026	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Possible tumor suppressor.;

Recessive Scores

pRec: 0.118

Intolerance Scores

LoFtool: 0.958
RVIS EVS: -1.5
RVIS percentile EVS: 3.57

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.359

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium